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billgreenwald / Pubmed-Batch-Download

Batch download articles based on PMID (Pubmed ID)
MIT License
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Trouble with Elsevier articles #14

Closed OgnjenMilicevic closed 5 years ago

OgnjenMilicevic commented 5 years ago

Hello!

I am having trouble downloading Elsevier papers, even though I can access them through my academic network. Here are the PMIDs:

30898248 29934065 28325353 28256256

I have many more. Any help you can give is greatly appreciated!

billgreenwald commented 5 years ago

Edited: The backend to the pubmed api seems to be blocking requests, which breaks everything -- I'll investigate and try to fix when I can

billgreenwald commented 5 years ago

Ok I fixed it but had to migrate to python3 in order to get it to work. I need to update the yml, readme instructions, and then push everything, but you should be able to expect an update sometime tomorrow that resolves this issue.

OgnjenMilicevic commented 5 years ago

Your responsiveness and efficiency are just amazing! Thank you!

billgreenwald commented 5 years ago

the new version is live -- let me know if it works. You will need to install the new version of python, but I updated the .yml so you can use it to make a new conda environment easily. Let me know if it works or if you have other questions.

OgnjenMilicevic commented 5 years ago

Hi, thanks for the update, but unfortunately it doesn't work for me. I am not sure if I can help you debug this further in any way? To specify, I have automatic access to Elsevier papers via my institution, and I can access them from the browser. The link for me for paper "30898248" is "https://www.sciencedirect.com/science/article/pii/S1936879818321319/pdfft?md5=5bd79a6cab6a0a842fe595eab73d8b8c&pid=1-s2.0-S1936879818321319-main.pdf".

Also, when I take this link and put it in a different browser, it asks me to select my institution: "https://www.sciencedirect.com/user/chooseorg?targetURL=%2Fscience%2Farticle%2Fpii%2FS1936879818321319%2Fpdfft"

Screen Shot 2019-06-14 at 2 38 22 PM

Could this be preventing the automated download? I only agree to it once per browser session, and afterwards I have no problem reading the pdfs in it.

billgreenwald commented 5 years ago

My university has access but we don't need to select our organization -- this is probably messing you up yes. What browser can you access them through without needing to select institution, and what browser do you need to select it in?

Also to help, can you try going via a browser to the site using the NCBI api? Use the URL

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id={0}&retmode=ref&cmd=prlinks

but sub in the pmid where it says {0}

billgreenwald commented 5 years ago

I am closing this unless I hear something new